Any ImageJ tools/plugins for micro CT quantitative analysis ?

[Cindy Sheen]

I am new to ImageJ. It seems to me that this software was initially developed for microscopy imaging. I am wondering if most tools/plugins also work well with micro CT data.

Thanks!





 

 

 

     
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[ctrueden]

Hi Cindy,

> It seems to me that this software was initially developed for
> microscopy imaging.

It was initially developed (as NIH Image) for gels. See this article for a
full historical perspective:

   http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2089.html

But at this point, ImageJ has been developing for decades and caters to a
very broad user base.

The Fiji project (http://fiji.sc/) focuses on microscopy and life sciences
in general, but is by no means limited to that. We are working to
incorporate much of the general-purpose software infrastructure of Fiji
into ImageJ2 (http://developer.imagej.net/).

> I am wondering if most tools/plugins also work well with micro CT
> data.

Many (most?) of the plugins in ImageJ and Fiji are general-purpose in
nature, and can work with whatever sorts of image data that you throw at
it. One of my collaborators who does image segmentation likes to point out
that most segmentation can be classified as either "blobs", "tubes" or
"clouds"—highly non-domain-specific! The point is that there is great
overlap of image processing techniques across different disciplines.

Perhaps someone else on the list with a micro CT background can comment on
any specific challenges there with ImageJ.

HTH,
Curtis


On Thu, Feb 21, 2013 at 3:21 PM, Cindy Sheen <[hidden email]>wrote:

> I am new to ImageJ. It seems to me that this software was initially
> developed for microscopy imaging. I am wondering if most tools/plugins also
> work well with micro CT data.
>
> Thanks!
>
>
>
>
>
>
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Doube-4]

Hi Cindy,

What Curtis said - plus there are domain-specific requirements to which particular software is tailored.

Another motivation to find a particular program is what you want to analyse in your images, and what your hypothesis is, rather than the particular method you used to generate your images.

Having done lots of XMT (and knowing lots of others who do too), I can say that ImageJ's generic functionality works just fine, and it helps a lot if you understand what it is that you are doing and why you are doing it. For XMT-tailored analysis (aimed at bone, but fine for rock, cake, etc.) check out BoneJ http://bonej.org/ , which was originally put together to analyse XMT and CT images.

Michael

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Cindy Sheen [[hidden email]]
Sent: 21 February 2013 21:21
To: [hidden email]
Subject: Any ImageJ tools/plugins for micro CT quantitative analysis ?

I am new to ImageJ. It seems to me that this software was initially developed for microscopy imaging. I am wondering if most tools/plugins also work well with micro CT data.

Thanks!












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[robert atwood]

We use it all the time at Diamond beamline I12-JEEP , just as it is; sometimes Fiji primarily to have Jython scripting already built in. Visiting users can use it, are often familiar with it already, and they can easily get their own copy too if they aren't. It handles most data formats we can throw at it (though I couldn't so far get HDF5 to work )

the available tools are often a good first approach to a quick analysis whereas often the full analysis that the researchers need to do requires that they write their own programs (often in Matlab or something like that) because they are so specific to their experiment.  Sometimes, a plugin that's available in the collections e.g. MosaicJ  or particle tracking, is useful to some people.

With 3-d datasets, you just have to be careful about memory use; firstly get a computer with lots of memory, then configure Imagej or Fiji to use it. Then still be careful about requesting to load a 3-d dataset that is too big -- we can do this with our 120-Gb datasets even on the workstation with 96 Gb installed.

'Virtual Stack' is your friend! Also getting a biggish SSD installed on the workstation helps. They're not so expensive any more



We use other tools when rendering 3-d movies , e.g. free software Drishti from ANUSF VizLab, and some commercial packages.  3-d particle size measurement needs other software so far as far as I know , the ITK kit is good for processing of 3-d datasets but then Imagej is still pretty good for looking at the output results of any stand-alone 3-d data filters; perhaps someone has made a link via Java interface to ITK filters?

I find we often have to run 3-d image filters on a cluster anyways so having them integrated into visualization software just hampers the usability.  (Headless IJ should be very useful in this case too though I didn't get around to trying it yet)

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: 21 February 2013 21:57
> To: [hidden email]
> Subject: Re: Any ImageJ tools/plugins for micro CT quantitative
> analysis ?
>
> Hi Cindy,
>
> > It seems to me that this software was initially developed for
> > microscopy imaging.
>
> It was initially developed (as NIH Image) for gels. See this article
> for a full historical perspective:
>
>    http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2089.html
>
> But at this point, ImageJ has been developing for decades and caters to
> a very broad user base.
>
> The Fiji project (http://fiji.sc/) focuses on microscopy and life
> sciences in general, but is by no means limited to that. We are working
> to incorporate much of the general-purpose software infrastructure of
> Fiji into ImageJ2 (http://developer.imagej.net/).
>
> > I am wondering if most tools/plugins also work well with micro CT
> > data.
>
> Many (most?) of the plugins in ImageJ and Fiji are general-purpose in
> nature, and can work with whatever sorts of image data that you throw
> at it. One of my collaborators who does image segmentation likes to
> point out that most segmentation can be classified as either "blobs",
> "tubes" or "clouds"-highly non-domain-specific! The point is that there
> is great overlap of image processing techniques across different
> disciplines.
>
> Perhaps someone else on the list with a micro CT background can comment
> on any specific challenges there with ImageJ.
>
> HTH,
> Curtis
>
>
> On Thu, Feb 21, 2013 at 3:21 PM, Cindy Sheen
> <[hidden email]>wrote:
>
> > I am new to ImageJ. It seems to me that this software was initially
> > developed for microscopy imaging. I am wondering if most
> tools/plugins
> > also work well with micro CT data.
> >
> > Thanks!
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Cindy Sheen]

Hi Curtis,

Thank you very much for your answer! Very helpful. I appreciate it.


 

 

 

 

> Date: Thu, 21 Feb 2013 15:56:31 -0600
> From: [hidden email]
> Subject: Re: Any ImageJ tools/plugins for micro CT quantitative analysis ?
> To: [hidden email]
>
> Hi Cindy,
>
> > It seems to me that this software was initially developed for
> > microscopy imaging.
>
> It was initially developed (as NIH Image) for gels. See this article for a
> full historical perspective:
>
>    http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2089.html
>
> But at this point, ImageJ has been developing for decades and caters to a
> very broad user base.
>
> The Fiji project (http://fiji.sc/) focuses on microscopy and life sciences
> in general, but is by no means limited to that. We are working to
> incorporate much of the general-purpose software infrastructure of Fiji
> into ImageJ2 (http://developer.imagej.net/).
>
> > I am wondering if most tools/plugins also work well with micro CT
> > data.
>
> Many (most?) of the plugins in ImageJ and Fiji are general-purpose in
> nature, and can work with whatever sorts of image data that you throw at
> it. One of my collaborators who does image segmentation likes to point out
> that most segmentation can be classified as either "blobs", "tubes" or
> "clouds"—highly non-domain-specific! The point is that there is great
> overlap of image processing techniques across different disciplines.
>
> Perhaps someone else on the list with a micro CT background can comment on
> any specific challenges there with ImageJ.
>
> HTH,
> Curtis
>
>
> On Thu, Feb 21, 2013 at 3:21 PM, Cindy Sheen <[hidden email]>wrote:
>
> > I am new to ImageJ. It seems to me that this software was initially
> > developed for microscopy imaging. I am wondering if most tools/plugins also
> > work well with micro CT data.
> >
> > Thanks!
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

     
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Cindy Sheen]

Hi Michael,

Thanks a lot for your answer! I appreciate it.  We are not looking at bones. We look at segmentation work of organs like brain, eyes, gut ... (it will be great if it does not need much manual input) , and to extract some quantitative data at different levels ( organs, tissues, cells) such as number of cells and their geometric information for phenotypic characterization. Looks like Fiji is the software that can help us with this.


 Cindy

 

 

 

> Date: Fri, 22 Feb 2013 11:21:15 +0000
> From: [hidden email]
> Subject: Re: Any ImageJ tools/plugins for micro CT quantitative analysis ?
> To: [hidden email]
>
> Hi Cindy,
>
> What Curtis said - plus there are domain-specific requirements to which particular software is tailored.
>
> Another motivation to find a particular program is what you want to analyse in your images, and what your hypothesis is, rather than the particular method you used to generate your images.
>
> Having done lots of XMT (and knowing lots of others who do too), I can say that ImageJ's generic functionality works just fine, and it helps a lot if you understand what it is that you are doing and why you are doing it. For XMT-tailored analysis (aimed at bone, but fine for rock, cake, etc.) check out BoneJ http://bonej.org/ , which was originally put together to analyse XMT and CT images.
>
> Michael
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Cindy Sheen [[hidden email]]
> Sent: 21 February 2013 21:21
> To: [hidden email]
> Subject: Any ImageJ tools/plugins for micro CT quantitative analysis ?
>
> I am new to ImageJ. It seems to me that this software was initially developed for microscopy imaging. I am wondering if most tools/plugins also work well with micro CT data.
>
> Thanks!
>
>
>
>
>
>
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> [http://www.rvc.ac.uk/cf_images/button_rvc.png]<http://www.rvc.ac.uk>    [http://www.rvc.ac.uk/cf_images/button_twitter.png] <http://twitter.com/RoyalVetCollege>     [http://www.rvc.ac.uk/cf_images/button_facebook.png] <http://www.facebook.com/theRVC>
>
> This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

     
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